Index: head/biology/bowtie2/Makefile =================================================================== --- head/biology/bowtie2/Makefile (revision 499543) +++ head/biology/bowtie2/Makefile (revision 499544) @@ -1,55 +1,55 @@ # $FreeBSD$ PORTNAME= bowtie2 DISTVERSIONPREFIX= v -DISTVERSION= 2.3.5 +DISTVERSION= 2.3.5.1 CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Ultrafast, memory-efficient short read aligner LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE # May also work on other 64-bit platforms, but untested -ONLY_FOR_ARCHS= aarch64 amd64 -BROKEN_aarch64= usage: dirname string [...] - +ONLY_FOR_ARCHS= amd64 LIB_DEPENDS= libtbb.so:devel/tbb +RUN_DEPENDS= bash:shells/bash USES= gmake localbase:ldflags perl5 python shebangfix USE_PERL5= run USE_GITHUB= yes -SHEBANG_FILES= bowtie2 bowtie2-build bowtie2-inspect scripts/*.pl +SHEBANG_FILES= bowtie2 bowtie2-build bowtie2-inspect \ + scripts/bowtie2-hbb.sh scripts/*.pl GH_ACCOUNT= BenLangmead OPTIONS_DEFINE= DOCS EXAMPLES SUB_FILES= bowtie2-test pre-configure: @${REINPLACE_CMD} \ -e 's|^RELEASE_FLAGS|# RELEASE_FLAGS|' \ -e 's|tbbmalloc_proxy|tbbmalloc|' \ ${WRKSRC}/Makefile post-install: @${MKDIR} ${STAGEDIR}${DATADIR}/scripts ${INSTALL_PROGRAM} \ ${WRKSRC}/bowtie2*-s \ ${WRKSRC}/bowtie2*-l \ ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} \ ${WRKSRC}/scripts/*.sh \ ${WRKSRC}/scripts/*.pl \ ${STAGEDIR}${DATADIR}/scripts ${INSTALL_SCRIPT} ${WRKDIR}/bowtie2-test ${STAGEDIR}${PREFIX}/bin post-install-DOCS-on: (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) post-install-EXAMPLES-on: (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) .include Index: head/biology/bowtie2/distinfo =================================================================== --- head/biology/bowtie2/distinfo (revision 499543) +++ head/biology/bowtie2/distinfo (revision 499544) @@ -1,3 +1,3 @@ -TIMESTAMP = 1552832567 -SHA256 (BenLangmead-bowtie2-v2.3.5_GH0.tar.gz) = c5daeb0249e98dfe8f70dac7d660b100365a00a22df4cad94d3e383f489911ae -SIZE (BenLangmead-bowtie2-v2.3.5_GH0.tar.gz) = 10584383 +TIMESTAMP = 1555781941 +SHA256 (BenLangmead-bowtie2-v2.3.5.1_GH0.tar.gz) = 86a018af1090900c160a0990cc106569805aa64a3ec8708e1d2127839e4a94b4 +SIZE (BenLangmead-bowtie2-v2.3.5.1_GH0.tar.gz) = 10587039 Index: head/biology/bowtie2/files/patch-Makefile =================================================================== --- head/biology/bowtie2/files/patch-Makefile (revision 499543) +++ head/biology/bowtie2/files/patch-Makefile (revision 499544) @@ -1,24 +1,52 @@ ---- Makefile.orig 2019-03-16 04:14:43 UTC +--- Makefile.orig 2019-04-17 02:40:25 UTC +++ Makefile @@ -21,8 +21,9 @@ # Makefile for bowtie, bowtie2-build, bowtie2-inspect # -prefix := /usr/local -bindir := $(prefix)/bin +# Use PREFIX (upper case) provided by many package managers -+PREXIX ?= /usr/local ++PREFIX ?= /usr/local +bindir := $(PREFIX)/bin LDLIBS := -lz GCC_PREFIX := $(shell dirname `which gcc`) -@@ -30,7 +31,8 @@ GCC_SUFFIX := +@@ -30,8 +31,9 @@ GCC_SUFFIX := CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) CXX ?= $(CPP) -CXXFLAGS += -std=c++98 +-ifeq (aarch64,$(shell uname -m)) +# long long is unsupported in c++98 +# CXXFLAGS += -std=c++98 - ifeq (aarch64,$(shell uname -m)) - CXXFLAGS += -fopenmp-simd -DWITH_AARCH64 ++ifeq (aarch64,$(shell uname -p)) + CXXFLAGS += -fopenmp-simd CPPFLAGS += -Ithird_party/simde + endif +@@ -198,13 +200,13 @@ SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c) + VERSION := $(shell cat VERSION) + + BITS := 32 +-ifeq (x86_64,$(shell uname -m)) ++ifeq (x86_64,$(shell uname -p)) + BITS := 64 + endif +-ifeq (amd64,$(shell uname -m)) ++ifeq (amd64,$(shell uname -p)) + BITS := 64 + endif +-ifeq (aarch64,$(shell uname -m)) ++ifeq (aarch64,$(shell uname -p)) + BITS := 64 + endif + # msys will always be 32 bit so look at the cpu arch instead. +@@ -219,7 +221,7 @@ endif + + SSE_FLAG := -msse2 + M64_FLAG := -m64 +-ifeq (aarch64,$(shell uname -m)) ++ifeq (aarch64,$(shell uname -p)) + SSE_FLAG = + M64_FLAG = + endif Index: head/biology/bowtie2/pkg-plist =================================================================== --- head/biology/bowtie2/pkg-plist (revision 499543) +++ head/biology/bowtie2/pkg-plist (revision 499544) @@ -1,66 +1,67 @@ bin/bowtie2 bin/bowtie2-align-l bin/bowtie2-align-s bin/bowtie2-build bin/bowtie2-build-l bin/bowtie2-build-s bin/bowtie2-inspect bin/bowtie2-inspect-l bin/bowtie2-inspect-s bin/bowtie2-test +%%DATADIR%%/scripts/bowtie2-hbb.sh %%DATADIR%%/scripts/convert_quals.pl %%DATADIR%%/scripts/gen_2b_occ_lookup.pl %%DATADIR%%/scripts/gen_occ_lookup.pl %%DATADIR%%/scripts/gen_solqual_lookup.pl %%DATADIR%%/scripts/infer_fraglen.pl %%DATADIR%%/scripts/make_a_thaliana_tair.sh %%DATADIR%%/scripts/make_b_taurus_UMD3.sh %%DATADIR%%/scripts/make_c_elegans.sh %%DATADIR%%/scripts/make_canFam2.sh %%DATADIR%%/scripts/make_d_melanogaster.sh %%DATADIR%%/scripts/make_e_coli.sh %%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh %%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh %%DATADIR%%/scripts/make_hg18.sh %%DATADIR%%/scripts/make_hg19.sh %%DATADIR%%/scripts/make_m_musculus_ncbi37.sh %%DATADIR%%/scripts/make_mm10.sh %%DATADIR%%/scripts/make_mm9.sh %%DATADIR%%/scripts/make_rn4.sh %%DATADIR%%/scripts/make_s_cerevisiae.sh %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/images/bowtie_logo.png %%PORTDOCS%%%%DOCSDIR%%/images/osi-certified.gif %%PORTDOCS%%%%DOCSDIR%%/images/sflogo.png %%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png %%PORTDOCS%%%%DOCSDIR%%/manual.html %%PORTDOCS%%%%DOCSDIR%%/release.txt %%PORTDOCS%%%%DOCSDIR%%/style.css %%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml %%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi %%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi %%PORTDOCS%%%%DOCSDIR%%/website/index.html %%PORTDOCS%%%%DOCSDIR%%/website/index.shtml %%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml %%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi %%PORTDOCS%%%%DOCSDIR%%/website/news.shtml %%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml %%PORTDOCS%%%%DOCSDIR%%/website/push.sh %%PORTDOCS%%%%DOCSDIR%%/website/push_images.sh %%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi %%PORTDOCS%%%%DOCSDIR%%/website/top.ssi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.1.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.2.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.3.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.4.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.1.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.2.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/combined_reads.bam %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/conversion_utilities.sh %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/longreads.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_1.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_2.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/simulate.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reference/lambda_virus.fa